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Hybrid Feature Factored System for Scoring Extracted Passage Relevance in Regulatory Filings

D. Proux, C. Roux, A. Sándor, J. Perez
2017 Proceedings of the 3rd International Workshop on Data Science for Macro--Modeling with Financial and Economic Datasets - DSMM'17  
We report in this paper our contribution to the FEIII 2017 challenge addressing relevance ranking of passages extracted from 10-K and 10-Q regulatory filings.  ...  We leveraged our previous work on document structure and content analysis for regulatory filings to train hybrid text analytics and decision making models.  ...  Hybrid Feature Factored System for Scoring Extracted Passage Relevance in Regulatory Filings DSMM / FEIII 2017, May 14 2017, Chicago, Illinois USA complement) to the first company name in the sentence,  ... 
doi:10.1145/3077240.3077251 dblp:conf/sigmod/ProuxRSP17 fatcat:ne5llfpx5ndp5d6nvwbe53kqiu

Knowledge Graph – Deep Learning: A Case Study in Question Answering in Aviation Safety Domain [article]

Ankush Agarwal, Raj Gite, Shreya Laddha, Pushpak Bhattacharyya, Satyanarayan Kar, Asif Ekbal, Prabhjit Thind, Rajesh Zele, Ravi Shankar
2022 arXiv   pre-print
There is a need for a system to access these diverse repositories efficiently in order to service needs in the aviation industry, like maintenance, compliance, and safety.  ...  In this paper, we propose a Knowledge Graph (KG) guided Deep Learning (DL) based Question Answering (QA) system for aviation safety.  ...  In this model, BM25 (Robertson and Zaragoza, 2009) relevance score is used for retrieving most relevant passages using sparse lexical features like TF-IDF.  ... 
arXiv:2205.15952v1 fatcat:5op3ptn7d5g55egz6zuy5isoey

The Protein-Protein Interaction tasks of BioCreative III: classification/ranking of articles and linking bio-ontology concepts to full text

Martin Krallinger, Miguel Vazquez, Florian Leitner, David Salgado, Andrew Chatr-aryamontri, Andrew Winter, Livia Perfetto, Leonardo Briganti, Luana Licata, Marta Iannuccelli, Luisa Castagnoli, Gianni Cesareni (+22 others)
2011 BMC Bioinformatics  
In case of competitive systems with an acceptable recall (above 35) the macro-averaged precision ranged between 50 and 80, with a maximum F-Score of 55.  ...  by providing ranked results, textual evidence for human interpretation or measuring time savings by using automated systems.  ...  We would like to thank Reverse Informatics and in particular Parthiban Srinivasan for their collaboration on the ACT.  ... 
doi:10.1186/1471-2105-12-s8-s3 pmid:22151929 pmcid:PMC3269938 fatcat:vireubnikbhgjg2y2fskgqvgse

Overview of the protein-protein interaction annotation extraction task of BioCreative II

Martin Krallinger, Florian Leitner, Carlos Rodriguez-Penagos, Alfonso Valencia
2008 Genome Biology  
A total of 26 teams submitted runs for at least one of the proposed subtasks. In the interaction article detection subtask, the top scoring team reached an F-score of 0.78.  ...  As for the retrieval of the PPI passages best summarizing a given protein interaction in full-text articles, 19% of the submissions returned by one of the runs corresponded to curator-selected sentences  ...  This article has been published as part of Genome Biology Volume 9 Supplement 2, 2008: The BioCreative II -Critical Assessment for Information Extraction in Biology Challenge.  ... 
doi:10.1186/gb-2008-9-s2-s4 pmid:18834495 pmcid:PMC2559988 fatcat:hx656lrmsrbrpb2yb7ny3e75mu

A cultured approach to canine urothelial carcinoma: molecular characterization of five cell lines

SG Shapiro, DW Knapp, Matthew Breen
2015 Canine Genetics and Epidemiology  
In the present study, we evaluated five canine UC cell lines via oligonucleotide array comparative genomic hybridization (oaCGH), fluorescence in situ hybridization (FISH), and gene expression analysis  ...  Moreover, the cell lines may provide a valuable model for furthering our understanding of aberrant metabolic pathways in UC development.  ...  Arrays were scanned at 3 μm (Agilent, Model G2505C) and data extracted with Feature Extraction software (v10.9 Agilent) using the canFam2 genome build.  ... 
doi:10.1186/s40575-015-0028-3 pmid:26401343 pmcid:PMC4579363 fatcat:2cdo2zjj7fdrzclc7hv5f45334

RNA Enrichment Method for Quantitative Transcriptional Analysis of Pathogens In Vivo Applied to the Fungus Candida albicans

Sara Amorim-Vaz, Van Du T. Tran, Sylvain Pradervand, Marco Pagni, Alix T. Coste, Dominique Sanglard
2015 mBio  
We aimed to address the transcriptome profiles of Candida albicans , the most prevalent fungal pathogen in systemically infected immunocompromised patients, during systemic infection in different hosts  ...  We developed a strategy for high-resolution quantitative analysis of the C. albicans transcriptome directly from early and late stages of systemic infection in two different host models, mouse and the  ...  A machine-learning approach contributed to the establishment of the relevant gene features and numerical thresholds for gene rejection criteria.  ... 
doi:10.1128/mbio.00942-15 pmid:26396240 pmcid:PMC4600103 fatcat:v5seip6pl5d6xpo6iaonw6c3c4

MicroRNA-363 negatively regulates the left ventricular determining transcription factor HAND1 in human embryonic stem cell-derived cardiomyocytes

Vilas Wagh, Alexander Pomorski, Karlijn J Wilschut, Sebastian Piombo, Harold S Bernstein
2014 Stem Cell Research & Therapy  
Expression of anti-miR-363 in-vitro resulted in enrichment for HAND1-expressing CM subtype populations.  ...  We studied the temporal and spatial expression patterns of four miRNAs in differentiating hESCs, and found that expression of miRNA (miR)-363, miR-367, miR-181a, and miR-181c was specific for stage and  ...  Richards for technical assistance, and Suzanne Chen for editorial assistance during the preparation of this manuscript.  ... 
doi:10.1186/scrt464 pmid:24906886 pmcid:PMC4097848 fatcat:3v5pcl5vvvaqde2vxib6hrv7gy

Cell type-specific over-expression of chromosome 21 genes in fibroblasts and fetal hearts with trisomy 21

Chi-Ming Li, Meirong Guo, Martha Salas, Nicole Schupf, Wayne Silverman, Warren B Zigman, Sameera Husain, Dorothy Warburton, Harshwardhan Thaker, Benjamin Tycko
2006 BMC Medical Genetics  
Hyperactive interferon signaling is a candidate pathway for cell senescence and autoimmune disorders in DS, and abnormal purine metabolism should be investigated for a potential role in cardiac defects  ...  Conclusion: Different subsets of chromosome 21 genes are over-expressed in different cell types with +21, and for some genes this over-expression is non-linear (>1.5X).  ...  Acknowledgements We thank Otto Haller for anti-p78 MX1 antibody and Giorgio Cattoretti for advice on immunohistochemistry.  ... 
doi:10.1186/1471-2350-7-24 pmid:16539728 pmcid:PMC1435874 fatcat:piv3jnntjrcjzoaevvopp7h6iy

A panel of induced pluripotent stem cells from chimpanzees: a resource for comparative functional genomics

Irene Gallego Romero, Bryan J Pavlovic, Irene Hernando-Herraez, Xiang Zhou, Michelle C Ward, Nicholas E Banovich, Courtney L Kagan, Jonathan E Burnett, Constance H Huang, Amy Mitrano, Claudia I Chavarria, Inbar Friedrich Ben-Nun (+8 others)
2015 eLife  
In order to gain better insight into the genetic processes that underlie variation in complex phenotypes in primates, we must have access to faithful model systems for a wide range of cell types.  ...  The low within-species regulatory variation in iPSCs allowed us to identify many novel inter-species regulatory differences of small magnitude.  ...  All PCRs were carried out on templates 913 extracted from passage >15 with the exception of C3651*, which is from passage 2.  ... 
doi:10.7554/elife.07103 pmid:26102527 pmcid:PMC4502404 fatcat:uy2b7gg52zdjff7zllawntdpbq

Novel application of multi-stimuli network inference to synovial fibroblasts of rheumatoid arthritis patients

Peter Kupfer, René Huber, Michael Weber, Sebastian Vlaic, Thomas Häupl, Dirk Koczan, Reinhard Guthke, Raimund W Kinne
2014 BMC Medical Genomics  
The selected GO term 'cartilage development' contained a number of differentiation markers, growth factors, and transcription factors with potential relevance for RA.  ...  Network inference of gene expression data is an important challenge in systems biology.  ...  This allows to reduce the effects of cross-hybridization and other system-based biases [30] [31] [32] [33] .  ... 
doi:10.1186/1755-8794-7-40 pmid:24989895 pmcid:PMC4099018 fatcat:izprspitabcohmsun7izo2pry4

Analysis of Control Security and Privacy Based on e-Learning Users

Husain T., Agus Budiyantara
2020 SAR Journal  
The study objective is to analyze the control of security and privacy, the theory of planned behavior (TPB), i.e. attitude and behavioral intention factors to support the e-Learning users in Pamulang University  ...  Attitude and behavioral intention are an intervening variable in the effect of the control of security and privacy on e- Learning users.  ...  These results confirm the importance of the control Security and Privacy regulatory factors in predicting attitudes and behavioral intention models for e-Learning users.  ... 
doi:10.18421/sar32-01 fatcat:et3d7c45k5d5tjhv2srsyixmre

Global target mRNA specification and regulation by the RNA-binding protein ZFP36

Neelanjan Mukherjee, Nicholas C Jacobs, Markus Hafner, Elizabeth A Kennington, Jeffrey D Nusbaum, Thomas Tuschl, Perry J Blackshear, Uwe Ohler
2014 Genome Biology  
Genes with increased mRNA half-lives in ZFP36 knockout versus wild-type mouse cells were significantly enriched for our human ZFP36 targets.  ...  ZFP36, also known as tristetraprolin or TTP, and ELAVL1, also known as HuR, are two disease-relevant RNA-binding proteins (RBPs) that both interact with AU-rich sequences but have antagonistic roles.  ...  We would like to acknowledge Jack Keene for very insightful early discussions and suggestions.  ... 
doi:10.1186/gb-2014-15-1-r12 pmid:24401661 pmcid:PMC4053807 fatcat:gddznewbcnhxzjlxnlwk2hd5ba

Gene expression modifications in Wharton's Jelly mesenchymal stem cells promoted by prolonged in vitro culturing

Valentina Gatta, Marco D'Aurora, Paola Lanuti, Laura Pierdomenico, Samantha Sperduti, Giandomenico Palka, Marco Gesi, Marco Marchisio, Sebastiano Miscia, Liborio Stuppia
2013 BMC Genomics  
12 passages of in vitro expansion by microarray analysis.  ...  The easy access to massive WJ amount makes it an attractive source of MSCs for cell-based therapies.  ...  Amplified aRNAs were used for microarray experiments carried out by hybridization of WJ-MSCs after 4 passages, compared to WJ-MSCs after 12 passages, for a total of 6 experiments ( Table 1 ).  ... 
doi:10.1186/1471-2164-14-635 pmid:24053474 pmcid:PMC3849041 fatcat:4knhhsl6wjg3xml5wefs2e64tm

Alice Krebs, Tanja Waldmann, Martin F. Wilks, Barbara M. A. van Vugt-Lussenburg, Bart van der Burg, Andrea Terron, Thomas Steger-Hartmann, Joelle Ruegg, Costanza Rovida, Emma Pedersen, Giorgia Pallocca, Mirjam Luijten (+24 others)
2019 ALTEX: Alternatives to Animal Experimentation  
Moreover, little attention was given to the description of the test system (i.e., cell culture) and the steps leading to it being established in the guidance.  ...  Only few cell-based test methods are described by Organisation for Economic Co-operation and Development (OECD) test guidelines or other regulatory references (e.g., the European Pharmacopoeia).  ...  Alternatives to Animal Testing) of the Ministry for Culture and Science of the State of North-Rhine Westphalia, Germany [233-].  ... 
doi:10.14573/altex.1909271 pmid:31658359 fatcat:vkqls4lldve57gqfkddi2qcipi

Developing and applying a gene functional association network for anti-angiogenic kinase inhibitor activity assessment in an angiogenesis co-culture model

Yuefeng Chen, Tao Wei, Lei Yan, Frank Lawrence, Hui-Rong Qian, Timothy P Burkholder, James J Starling, Jonathan M Yingling, Jianyong Shou
2008 BMC Genomics  
HUVEC competence and NHDF supportiveness of cord formation were found to be highly cell-passage dependent.  ...  We developed a network walking algorithm to extract connectivity information from the interactome and applied it to simulate the level of network perturbation by three multi-targeted anti-angiogenic kinase  ...  We would also like to extend our thanks to Karen Morgan for her assistance in preparing the manuscript.  ... 
doi:10.1186/1471-2164-9-264 pmid:18518970 pmcid:PMC2435557 fatcat:bt6pdnlwrzcvlhlipw7ihcajd4
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